Genomic surveillance identifies shared Salmonella clusters and antimicrobial resistance across dogs, raw pet food and humans

Abstract The emergence of antimicrobial resistant Salmonella poses growing public health challenges, with companion animals and their diets representing under recognised transmission routes. Despite increasing use of raw pet food (RPF) and statutory reporting of canine Salmonella infections, limited genomic data have been used to investigate potential transmission pathways and their implications for human health. In order to identify potential zoonotic links and characterise antimicrobial resistance, we conducted a genomic analysis of Salmonella spp. isolates from dogs ( n = 1,017) and raw meat pet food ( n = 206) collected between 2006 and 2024 through a collaborative surveillance programme. All isolates underwent whole genome sequencing (WGS), and comparative genomic analysis was performed against human clinical isolates. Among 1,223 sequenced isolates, 676 unique 5 SNP single linkage clusters, across 29 different Salmonella serovars were identified. Overall, 27.2% (148/545) of canine isolates and 23.7% (27/114) of RPF isolates were genetically related to human cases, with 88.2% (15/17) of shared dog–RPF isolates also clustering with human infections. Multi-drug resistant (MDR) strains, including those resistant to critically important antimicrobials, were detected in both dogs and RPF. Salmonella Typhimurium predominated across human and canine isolates including the distribution of MDR within multiple clusters. These findings highlight the zoonotic risk associated with dogs and raw pet food within domestic settings, underscoring the need for targeted public health messaging and strengthened One Health genomic surveillance.